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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $species_info = array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ) $local_species = 'ama' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $species_info = array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ) $local_species = 'ama' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $species_info = array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ) $local_species = 'cde' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $species_info = array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ) $local_species = 'cde' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $species_info = array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ) $local_species = 'cla' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $species_info = array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ) $local_species = 'cla' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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) 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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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) 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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $species_info = array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ) $local_species = 'eca' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $species_info = array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ) $local_species = 'eca' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $species_info = array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ) $local_species = 'ghi' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $species_info = array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ) $local_species = 'ghi' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $species_info = array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ) $local_species = 'mdo' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $species_info = array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ) $local_species = 'mdo' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $species_info = array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ) $local_species = 'nta' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $species_info = array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ) $local_species = 'nta' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $species_info = array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ) $local_species = 'ptr' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $species_info = array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ) $local_species = 'ptr' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $species_info = array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ) $local_species = 'rsi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $species_info = array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ) $local_species = 'rsi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $species_info = array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ) $local_species = 'sbr' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $species_info = array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ) $local_species = 'sbr' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $species_info = array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ) $local_species = 'sas' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $species_info = array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ) $local_species = 'sas' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $species_info = array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ) $local_species = 'tha' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $species_info = array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ) $local_species = 'tha' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $species_info = array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ) $local_species = 'tca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $species_info = array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ) $local_species = 'tca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $species_info = array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ) $local_species = 'twi' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $species_info = array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ) $local_species = 'twi' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $species_info = array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ) $local_species = 'vpl' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $species_info = array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ) $local_species = 'vpl' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $species_info = array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ) $local_species = 'vvi' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $species_info = array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ) $local_species = 'vvi' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ), 'gf_id' => 'ORTHO05D000994', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ), 'data_identifier' => 'ORTHO05D000994', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'ORTHO05D000994', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '526', 'num_species' => '60' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'Actinidia04699' => 'ach', 'Actinidia06122' => 'ach', 'Actinidia06124' => 'ach', 'Actinidia06703' => 'ach', 'Actinidia19718' => 'ach', 'Actinidia28275' => 'ach', 'Actinidia28289' => 'ach', 'Actinidia31092' => 'ach', 'Actinidia38178' => 'ach', 'Aqoxy4G02861' => 'aox', 'Aqoxy6G02446' => 'aox', 'Aqoxy7G02332' => 'aox', 'ATR0820G149' => 'atr', 'Atru.chr12.1294' => 'acertr', 'Atru.chr12.1575' => 'acertr', 'Atru.chr12.1576' => 'acertr', 'Atru.chr12.1584' => 'acertr', 'Atru.chr7.641' => 'acertr', 'CAN.G162.3' => 'can', 'CAN.G1871.3' => 'can', 'CAN.G534.1' => 'can', 'CAN.G556.4' => 'can', 'CAN.G894.1' => 'can', 'CAN.G92.26' => 'can', 'Cc00_g12380' => 'ccan', 'Cc01_g09650' => 'ccan', 'Cc02_g10010' => 'ccan', 'Cc02_g10020' => 'ccan', 'Cc02_g10030' => 'ccan', 'Cc02_g10040' => 'ccan', 'Cc02_g10050' => 'ccan', 'Cc03_g02270' => 'ccan', 'Cc06_g22610' => 'ccan', 'Cc07_g18000' => 'ccan', 'Cc07_g18010' => 'ccan', 'Cc07_g18030' => 'ccan', 'Cc07_g18040' => 'ccan', 'Cc08_g04700' => 'ccan', 'Cc10_g13030' => 'ccan', 'Cc10_g13040' => 'ccan', 'Cc10_g13060' => 'ccan', 'Cc10_g13070' => 'ccan', 'Cc11_g06140' => 'ccan', 'Cc11_g06150' => 'ccan', 'Cc11_g14430' => 'ccan', 'Cc11_g17190' => 'ccan', 'CDE02G2531' => 'cde', 'CDE04G2664' => 'cde', 'Cfa011237' => 'cfa', 'Cfa011238' => 'cfa', 'Ciclev10029858m.g' => 'ccl', 'Ciclev10030045m.g' => 'ccl', 'Ciclev10030271m.g' => 'ccl', 'Ciclev10033373m.g' => 'ccl', 'Ciclev10033610m.g' => 'ccl', 'CiPaw.13G037000' => 'cil', 'CiPaw.13G037100' => 'cil', 'CiPaw.14G029300' => 'cil', 'ClCG02G024130' => 'cla', 'ClCG02G024140' => 'cla', 'ClCG05G021620' => 'cla', 'ClCG05G021640' => 'cla', 'ClCG08G008150' => 'cla', 'COL.COLO4_20113' => 'col', 'COL.COLO4_20116' => 'col', 'Cpa.g.sc19.19' => 'cpa', 'CsaV3_4G023190' => 'csa', 'CsaV3_4G023200' => 'csa', 'CsaV3_4G023220' => 'csa', 'CsaV3_6G004120' => 'csa', 'CsaV3_UNG234390' => 'csa', 'CsaV3_UNG234400' => 'csa', 'CsaV3_UNG234410' => 'csa', 'CSS0000389' => 'camsi', 'CSS0002110' => 'camsi', 'CSS0007255' => 'camsi', 'CSS0007733' => 'camsi', 'CSS0008350' => 'camsi', 'CSS0011196' => 'camsi', 'CSS0012277' => 'camsi', 'CSS0015472' => 'camsi', 'CSS0017126' => 'camsi', 'CSS0019095' => 'camsi', 'CSS0019479' => 'camsi', 'CSS0020394' => 'camsi', 'CSS0021985' => 'camsi', 'CSS0022792' => 'camsi', 'CSS0022802' => 'camsi', 'CSS0024992' => 'camsi', 'CSS0025403' => 'camsi', 'CSS0027505' => 'camsi', 'CSS0029555' => 'camsi', 'CSS0029726' => 'camsi', 'CSS0033369' => 'camsi', 'CSS0040800' => 'camsi', 'CSS0044253' => 'camsi', 'CSS0044625' => 'camsi', 'DCAR_006360' => 'dca', 'DCAR_006364' => 'dca', 'DCAR_006368' => 'dca', 'DCAR_012622' => 'dca', 'DCAR_012695' => 'dca', 'DCAR_016266' => 'dca', 'DCAR_018968' => 'dca', 'DCAR_018969' => 'dca', 'DCAR_026654' => 'dca', 'DCAR_029182' => 'dca', 'DCAR_031780' => 'dca', 'Dinv06793' => 'din', 'Dinv12512' => 'din', 'Dinv20812' => 'din', 'Dinv20815' => 'din', 'Dinv20816' => 'din', 'Dinv20818' => 'din', 'ECA236G2141' => 'eca', 'ECA236G3550' => 'eca', 'ECA236G4364' => 'eca', 'ECA240G0825' => 'eca', 'ECA240G2658' => 'eca', 'ECA240G4441' => 'eca', 'ECA246G4866' => 'eca', 'Eucgr.B03886' => 'egr', 'Eucgr.J00443' => 'egr', 'Eucgr.J00447' => 'egr', 'Eucgr.J01005' => 'egr', 'Eucgr.J01006' => 'egr', 'Eucgr.J01007' => 'egr', 'Eucgr.J01008' => 'egr', 'Eucgr.J01009' => 'egr', 'Eucgr.J01013' => 'egr', 'Eucgr.J01015' => 'egr', 'Eucgr.J02585' => 'egr', 'Gohir.A01G130500' => 'ghi', 'Gohir.A07G107833' => 'ghi', 'Gohir.A10G235500' => 'ghi', 'Gohir.D01G119400' => 'ghi', 'Gohir.D07G111750' => 'ghi', 'Gohir.D10G247900' => 'ghi', 'Gorai.001G120100' => 'gra', 'Gorai.002G145800' => 'gra', 'GSVIVG01026464001' => 'vvi', 'GSVIVG01034736001' => 'vvi', 'HanXRQChr03g0083491' => 'han', 'HanXRQChr17g0569111' => 'han', 'Hma1.2p1_0352F.1_g133090' => 'hma', 'Hma1.2p1_0761F.1_g214300' => 'hma', 'Hma1.2p1_1273F.1_g271910' => 'hma', 'HPP92_017670' => 'vpl', 'Lj2A29T75' => 'lonja', 'Lj2A29T77' => 'lonja', 'Lj2A29T78' => 'lonja', 'Lj2A29T79' => 'lonja', 'Lj2C28T0' => 'lonja', 'Lj2C28T1' => 'lonja', 'Lj2C28T2' => 'lonja', 'Lj2C28T3' => 'lonja', 'Lj2C29G4' => 'lonja', 'Lj2C991T17' => 'lonja', 'Lj3A930T62' => 'lonja', 'Lj3C930T11' => 'lonja', 'Lj6A670T86' => 'lonja', 'Lj6C670T22' => 'lonja', 'Lsat_1_v5_gn_4_3081' => 'lsa', 'Lsat_1_v5_gn_4_3121' => 'lsa', 'Lsat_1_v5_gn_4_3201' => 'lsa', 'Lsat_1_v5_gn_8_54560' => 'lsa', 'Lsat_1_v5_gn_8_54580' => 'lsa', 'Lsat_1_v5_gn_9_34661' => 'lsa', 'Manes.07G090000' => 'mes', 'MD02G1248100' => 'mdo', 'MD02G1248200' => 'mdo', 'MD02G1248300' => 'mdo', 'MD02G1248500' => 'mdo', 'MD07G1067600' => 'mdo', 'MD07G1067700' => 'mdo', 'MD07G1068000' => 'mdo', 'MELO3C001224.2' => 'cme', 'MELO3C014696.2' => 'cme', 'MELO3C014697.2' => 'cme', 'MELO3C019888.2' => 'cme', 'Migut.B01568' => 'egut', 'Migut.F00894' => 'egut', 'Migut.F01669' => 'egut', 'Migut.G00200' => 'egut', 'Migut.G00201' => 'egut', 'Migut.G00202' => 'egut', 'Migut.J01722' => 'egut', 'Migut.J01723' => 'egut', 'Migut.J01724' => 'egut', 'Migut.J01793' => 'egut', 'Migut.N00116' => 'egut', 'Migut.N00117' => 'egut', 'Migut.N00118' => 'egut', 'MSTRG.10061' => 'ama', 'MSTRG.10063' => 'ama', 'MSTRG.21810' => 'ama', 'MSTRG.21811' => 'ama', 'MSTRG.27522' => 'ama', 'MSTRG.3947' => 'ama', 'Nitab4.5_0000004g0020' => 'nta', 'Nitab4.5_0000123g0490' => 'nta', 'Nitab4.5_0000342g0300' => 'nta', 'Nitab4.5_0000452g0060' => 'nta', 'Nitab4.5_0000608g0050' => 'nta', 'Nitab4.5_0000755g0220' => 'nta', 'Nitab4.5_0000829g0110' => 'nta', 'Nitab4.5_0000962g0010' => 'nta', 'Nitab4.5_0000962g0020' => 'nta', 'Nitab4.5_0000962g0040' => 'nta', 'Nitab4.5_0000991g0130' => 'nta', 'Nitab4.5_0001016g0020' => 'nta', 'Nitab4.5_0001569g0010' => 'nta', 'Nitab4.5_0001931g0060' => 'nta', 'Nitab4.5_0002288g0050' => 'nta', 'Nitab4.5_0002318g0010' => 'nta', 'Nitab4.5_0002318g0030' => 'nta', 'Nitab4.5_0002318g0050' => 'nta', 'Nitab4.5_0002878g0040' => 'nta', 'Nitab4.5_0002986g0010' => 'nta', 'Nitab4.5_0003074g0070' => 'nta', 'Nitab4.5_0003185g0040' => 'nta', 'Nitab4.5_0003472g0080' => 'nta', 'Nitab4.5_0004361g0010' => 'nta', 'Nitab4.5_0004382g0030' => 'nta', 'Nitab4.5_0004382g0050' => 'nta', 'Nitab4.5_0005390g0040' => 'nta', 'Nitab4.5_0005390g0060' => 'nta', 'Nitab4.5_0005733g0030' => 'nta', 'Nitab4.5_0006355g0010' => 'nta', 'Nitab4.5_0007031g0020' => 'nta', 'Nitab4.5_0008432g0040' => 'nta', 'Nitab4.5_0008756g0010' => 'nta', 'Nitab4.5_0008853g0010' => 'nta', 'Nitab4.5_0009571g0010' => 'nta', 'Nitab4.5_0010063g0020' => 'nta', 'Nitab4.5_0010357g0020' => 'nta', 'Nitab4.5_0010633g0030' => 'nta', 'Nitab4.5_0011086g0020' => 'nta', 'Nitab4.5_0026891g0010' => 'nta', 'Nn6g35017' => 'nnu', 'Oeu010971.1' => 'oeu', 'Oeu015038.1' => 'oeu', 'Oeu015041.1' => 'oeu', 'Oeu021043.1' => 'oeu', 'Oeu026568.1' => 'oeu', 'Oeu029267.4' => 'oeu', 'Oeu029271.1' => 'oeu', 'Oeu029273.1' => 'oeu', 'Oeu030497.1' => 'oeu', 'Oeu061506.1' => 'oeu', 'Oeu061507.1' => 'oeu', 'Oeu061772.2' => 'oeu', 'Os07g0672700' => 'osa', 'Peaxi162Scf00003g00534' => 'pax', 'Peaxi162Scf00003g04132' => 'pax', 'Peaxi162Scf00024g00066' => 'pax', 'Peaxi162Scf00024g00616' => 'pax', 'Peaxi162Scf00030g00011' => 'pax', 'Peaxi162Scf00030g00015' => 'pax', 'Peaxi162Scf00038g00235' => 'pax', 'Peaxi162Scf00047g01421' => 'pax', 'Peaxi162Scf00065g00520' => 'pax', 'Peaxi162Scf00189g00055' => 'pax', 'Peaxi162Scf00207g00618' => 'pax', 'Peaxi162Scf00207g00939' => 'pax', 'Peaxi162Scf00244g00086' => 'pax', 'Peaxi162Scf00244g00910' => 'pax', 'Peaxi162Scf00244g00911' => 'pax', 'Peaxi162Scf00244g01119' => 'pax', 'Peaxi162Scf00253g00133' => 'pax', 'Peaxi162Scf00253g00137' => 'pax', 'Peaxi162Scf00253g00138' => 'pax', 'Peaxi162Scf00386g00926' => 'pax', 'Peaxi162Scf00393g00032' => 'pax', 'Peaxi162Scf00421g00420' => 'pax', 'Peaxi162Scf00565g00002' => 'pax', 'Peaxi162Scf03648g00019' => 'pax', 'Peaxi162Scf03917g00006' => 'pax', 'Peaxi162Scf03917g00007' => 'pax', 'Peaxi162Scf03917g00008' => 'pax', 'PGR044G0575' => 'pgr', 'PGR044G2345' => 'pgr', 'PGSC0003DMG400000103' => 'stu', 'PGSC0003DMG400002113' => 'stu', 'PGSC0003DMG400004526' => 'stu', 'PGSC0003DMG400008181' => 'stu', 'PGSC0003DMG400014932' => 'stu', 'PGSC0003DMG400016050' => 'stu', 'PGSC0003DMG400016051' => 'stu', 'PGSC0003DMG400017191' => 'stu', 'PGSC0003DMG400017249' => 'stu', 'PGSC0003DMG400017250' => 'stu', 'PGSC0003DMG400019093' => 'stu', 'PGSC0003DMG400019483' => 'stu', 'PGSC0003DMG400019484' => 'stu', 'PGSC0003DMG400019485' => 'stu', 'PGSC0003DMG400019497' => 'stu', 'PGSC0003DMG400019560' => 'stu', 'PGSC0003DMG400020895' => 'stu', 'PGSC0003DMG400020896' => 'stu', 'PGSC0003DMG400020897' => 'stu', 'PGSC0003DMG400020900' => 'stu', 'PGSC0003DMG400020901' => 'stu', 'PGSC0003DMG400020902' => 'stu', 'PGSC0003DMG400020903' => 'stu', 'PGSC0003DMG400022657' => 'stu', 'PGSC0003DMG400023385' => 'stu', 'PGSC0003DMG400023386' => 'stu', 'PGSC0003DMG400026560' => 'stu', 'PGSC0003DMG400027338' => 'stu', 'PGSC0003DMG400029130' => 'stu', 'PGSC0003DMG400029131' => 'stu', 'PGSC0003DMG400029132' => 'stu', 'PGSC0003DMG400029133' => 'stu', 'PGSC0003DMG400031454' => 'stu', 'PGSC0003DMG400034672' => 'stu', 'PGSC0003DMG400035383' => 'stu', 'PGSC0003DMG400037235' => 'stu', 'PGSC0003DMG400038267' => 'stu', 'PGSC0003DMG400038305' => 'stu', 'PGSC0003DMG400041076' => 'stu', 'PGSC0003DMG400041203' => 'stu', 'PGSC0003DMG400041532' => 'stu', 'PGSC0003DMG400042118' => 'stu', 'PGSC0003DMG400042232' => 'stu', 'PGSC0003DMG400042343' => 'stu', 'PGSC0003DMG400042829' => 'stu', 'PGSC0003DMG400043363' => 'stu', 'PGSC0003DMG400045814' => 'stu', 'PGSC0003DMG400046494' => 'stu', 'Potri.008G024801' => 'ptr', 'Potri.008G024900' => 'ptr', 'Prupe.2G084900' => 'ppe', 'Prupe.2G085000' => 'ppe', 'Prupe.2G085100' => 'ppe', 'Prupe.2G085200' => 'ppe', 'Prupe.2G085300' => 'ppe', 'Prupe.2G085700' => 'ppe', 'Prupe.2G085800' => 'ppe', 'Prupe.2G086000' => 'ppe', 'PSO384G2162' => 'pso', 'PSO384G2445' => 'pso', 'PSO384G3544' => 'pso', 'PSO443G0003' => 'pso', 'PSO443G0006' => 'pso', 'PSO443G0040' => 'pso', 'QL01p013421' => 'qlo', 'QL04p006680' => 'qlo', 'QL04p007917' => 'qlo', 'QL04p042266' => 'qlo', 'QL04p042279' => 'qlo', 'QL04p042386' => 'qlo', 'QL04p042430' => 'qlo', 'QL04p042468' => 'qlo', 'Rhsim01G0278300' => 'rsi', 'Rhsim03G0105100' => 'rsi', 'Rhsim03G0105200' => 'rsi', 'Rhsim03G0105300' => 'rsi', 'Rhsim04G0113400' => 'rsi', 'Rhsim05G0046700' => 'rsi', 'Rhsim09G0143400' => 'rsi', 'Rhsim09G0143500' => 'rsi', 'Rhsim09G0143600' => 'rsi', 'Rhsim09G0143700' => 'rsi', 'Rhsim09G0143900' => 'rsi', 'Rhsim09G0144000' => 'rsi', 'Rhsim09G0211200' => 'rsi', 'RhsimUnG0061400' => 'rsi', 'RhsimUnG0141200' => 'rsi', 'Sabra08G0016700' => 'sbr', 'SalBow1G2023' => 'sbo', 'SalBow2G0021' => 'sbo', 'SalBow2G0218' => 'sbo', 'SalBow2G0420' => 'sbo', 'SalBow2G1185' => 'sbo', 'SalBow2G1582' => 'sbo', 'SalBow2G1622' => 'sbo', 'SalBow2G1929' => 'sbo', 'SalBow2G2257' => 'sbo', 'SalBow2G2280' => 'sbo', 'SalBow2G2754' => 'sbo', 'SalBow3G3086' => 'sbo', 'SalBow3G3090' => 'sbo', 'SalBow3G4172' => 'sbo', 'SalBow3G4202' => 'sbo', 'SalBow4G2628' => 'sbo', 'SalBow5G2442' => 'sbo', 'SalBow5G2724' => 'sbo', 'SalBow5G3178' => 'sbo', 'SalBow5G3923' => 'sbo', 'SalBow5G5419' => 'sbo', 'SalBow5G5702' => 'sbo', 'SalBow6G2961' => 'sbo', 'SalBow6G5070' => 'sbo', 'SalBow6G5455' => 'sbo', 'Sed0003948' => 'sed', 'Sed0004435' => 'sed', 'Sed0008923' => 'sed', 'Sed0011261' => 'sed', 'Sed0016117' => 'sed', 'Sed0016188' => 'sed', 'Sed0016532' => 'sed', 'Sed0018209' => 'sed', 'Sed0021521' => 'sed', 'Sed0024283' => 'sed', 'Sed0025439' => 'sed', 'Sed0026232' => 'sed', 'Sed0026877' => 'sed', 'SEGI_02357' => 'sgi', 'SEGI_02934' => 'sgi', 'SEGI_04199' => 'sgi', 'SEGI_05427' => 'sgi', 'SEGI_07869' => 'sgi', 'SEGI_08272' => 'sgi', 'SEGI_08286' => 'sgi', 'SEGI_09695' => 'sgi', 'SEGI_12672' => 'sgi', 'SEGI_13579' => 'sgi', 'SEGI_13702' => 'sgi', 'SEGI_14207' => 'sgi', 'SEGI_15401' => 'sgi', 'SEGI_15685' => 'sgi', 'SEGI_16746' => 'sgi', 'SEGI_17369' => 'sgi', 'SEGI_18179' => 'sgi', 'SEGI_20654' => 'sgi', 'SEGI_21085' => 'sgi', 'SEGI_21438' => 'sgi', 'SEGI_22484' => 'sgi', 'SEGI_22863' => 'sgi', 'SEGI_23781' => 'sgi', 'SEGI_26794' => 'sgi', 'SEGI_30792' => 'sgi', 'SEGI_32928' => 'sgi', 'SEGI_33095' => 'sgi', 'SEGI_33164' => 'sgi', 'SEGI_33575' => 'sgi', 'SEGI_35645' => 'sgi', 'SEGI_36946' => 'sgi', 'SEGI_37402' => 'sgi', 'SEGI_37944' => 'sgi', 'SEGI_38173' => 'sgi', 'SEGI_40409' => 'sgi', 'SGA_v2.0_scaffold105G30459' => 'sas', 'SGA_v2.0_scaffold57G20207' => 'sas', 'SGA_v2.0_scaffold69G23088' => 'sas', 'SGA_v2.0_scaffold89G27546' => 'sas', 'SGA_v2.0_scaffold89G27551' => 'sas', 'SGA_v2.0_scaffold89G27574' => 'sas', 'SHI21281' => 'shi', 'SMO270G0049' => 'smo', 'Solyc01g067350.4' => 'sly', 'Solyc01g095760.3' => 'sly', 'Solyc02g065670.3' => 'sly', 'Solyc03g071850.1' => 'sly', 'Solyc03g078240.3' => 'sly', 'Solyc04g081830.1' => 'sly', 'Solyc05g005930.3' => 'sly', 'Solyc05g055343.2' => 'sly', 'Solyc07g043500.1' => 'sly', 'Solyc08g150105.1' => 'sly', 'Solyc09g089585.1' => 'sly', 'Solyc11g007350.1' => 'sly', 'Solyc11g007370.3' => 'sly', 'Solyc11g007380.1' => 'sly', 'Solyc11g007390.1' => 'sly', 'Solyc11g007450.3' => 'sly', 'Solyc11g007460.1' => 'sly', 'Solyc11g007470.1' => 'sly', 'Solyc11g007480.1' => 'sly', 'Solyc11g007490.1' => 'sly', 'Solyc11g007500.2' => 'sly', 'Sopen01g029230' => 'spe', 'Sopen01g039510' => 'spe', 'Sopen02g015890' => 'spe', 'Sopen03g019280' => 'spe', 'Sopen03g020960' => 'spe', 'Sopen04g035460' => 'spe', 'Sopen05g001960' => 'spe', 'Sopen05g033790' => 'spe', 'Sopen07g023080' => 'spe', 'Sopen08g004700' => 'spe', 'Sopen09g032510' => 'spe', 'Sopen09g032530' => 'spe', 'Sopen11g003240' => 'spe', 'Sopen11g003260' => 'spe', 'Sopen11g003270' => 'spe', 'Sopen11g003280' => 'spe', 'Sopen11g003300' => 'spe', 'Sopen11g003310' => 'spe', 'Sopen11g003320' => 'spe', 'Sopen11g003330' => 'spe', 'Sopen11g003340' => 'spe', 'TAR369G0021' => 'tar', 'TAR369G0093' => 'tar', 'TAR369G0138' => 'tar', 'TAR369G0262' => 'tar', 'TAR369G1003' => 'tar', 'TAR623G1085' => 'tar', 'TAR623G1479' => 'tar', 'TAR623G1601' => 'tar', 'TAR633G0433' => 'tar', 'TAR633G1239' => 'tar', 'THA.LOC104803462' => 'tha', 'Thecc.09G290000' => 'tca', 'TWI15G0154' => 'twi', 'TWI15G0823' => 'twi', 'TWI15G0964' => 'twi', 'TWI79G0182' => 'twi', 'unitig_52.g17331' => 'ugi', 'vmacro10174' => 'vma', 'vmacro10279' => 'vma', 'vmacro10280' => 'vma', 'vmacro10281' => 'vma', 'vmacro10283' => 'vma', 'vmacro10284' => 'vma', 'vmacro10285' => 'vma', 'vmacro10287' => 'vma', 'vmacro10288' => 'vma', 'vmacro10289' => 'vma', 'vmacro10293' => 'vma', 'vmacro10294' => 'vma', 'vmacro10295' => 'vma', 'vmacro17307' => 'vma', 'Zm00001eb111270' => 'zma', 'Zm00001eb330430' => 'zma' ) $gf_id = 'ORTHO05D000994' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'ORTHO05D000994' ) $data_identifier = 'ORTHO05D000994' $data_type = 'gf_id' $species_gene_counts = array( 'ach' => (int) 9, 'aox' => (int) 3, 'atr' => (int) 1, 'acertr' => (int) 5, 'can' => (int) 6, 'ccan' => (int) 22, 'cde' => (int) 2, 'cfa' => (int) 2, 'ccl' => (int) 5, 'cil' => (int) 3, 'cla' => (int) 5, 'col' => (int) 2, 'cpa' => (int) 1, 'csa' => (int) 7, 'camsi' => (int) 24, 'dca' => (int) 11, 'din' => (int) 6, 'eca' => (int) 7, 'egr' => (int) 11, 'ghi' => (int) 6, 'gra' => (int) 2, 'vvi' => (int) 2, 'han' => (int) 2, 'hma' => (int) 3, 'vpl' => (int) 1, 'lonja' => (int) 14, 'lsa' => (int) 6, 'mes' => (int) 1, 'mdo' => (int) 7, 'cme' => (int) 4, 'egut' => (int) 13, 'ama' => (int) 6, 'nta' => (int) 40, 'nnu' => (int) 1, 'oeu' => (int) 12, 'osa' => (int) 1, 'pax' => (int) 27, 'pgr' => (int) 2, 'stu' => (int) 48, 'ptr' => (int) 2, 'ppe' => (int) 8, 'pso' => (int) 6, 'qlo' => (int) 8, 'rsi' => (int) 15, 'sbr' => (int) 1, 'sbo' => (int) 25, 'sed' => (int) 13, 'sgi' => (int) 35, 'sas' => (int) 6, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 21, 'spe' => (int) 21, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 1, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 14, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb330430' $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